Medina Nicolas, Tank David C, Espíndola Anahí
Department of Entomology University of Maryland College Park Maryland 20742-4454 USA.
Department of Botany and Rocky Mountain Herbarium University of Wyoming Laramie Wyoming 82071 USA.
Appl Plant Sci. 2023 Dec 2;11(6):e11557. doi: 10.1002/aps3.11557. eCollection 2023 Nov-Dec.
The genus (Calceolariaceae) is emblematic of the Andes, is hypothesized to have originated as a recent, rapid radiation, and has important taxonomic needs. Additionally, the genus is a model for the study of specialized pollination systems, as its flowers are nectarless and many offer floral oils as a pollination reward collected by specialist bees. Despite their evolutionary and ecological significance, obtaining a resolved phylogeny for the group has proved difficult. To address this challenge, we present a new bait set for targeted sequencing of nuclear loci in Calceolariaceae and close relatives.
We developed a bioinformatic workflow to use incomplete, low-coverage genomes of 10 species to identify single-copy loci suitable for phylogenetic studies and design baits for targeted sequencing.
Our approach resulted in the identification of 809 single-copy loci (733 noncoding and 76 coding regions) and the development of 39,937 baits, which we validated in silico (10 specimens) and in vitro (29 Calceolariaceae and six outgroups). In both cases, the data allowed us to recover robust phylogenetic estimates.
Our results demonstrate the appropriateness of the bait set for sequencing recent and historic specimens of Calceolariaceae and close relatives, and open new doors for further investigation of the evolutionary history of this hyperdiverse genus.
蒲包花属（荷包花科）是安第斯山脉的标志性植物，据推测它起源于近期的快速辐射演化，并且有重要的分类学需求。此外，该属是研究特殊授粉系统的一个模型，因为其花朵无花蜜，许多种类提供花油作为授粉报酬，由专门的蜜蜂采集。尽管它们具有进化和生态意义，但为该类群获得一个可靠的系统发育树却很困难。为应对这一挑战，我们提出了一套新的诱饵组，用于对荷包花科及其近缘类群的核基因座进行靶向测序。
我们开发了一种生物信息学工作流程，利用10个物种的不完整、低覆盖度基因组来识别适合系统发育研究的单拷贝基因座，并设计用于靶向测序的诱饵。
我们的方法鉴定出809个单拷贝基因座（733个非编码区和76个编码区），并开发了39937个诱饵，我们在计算机模拟（10个样本）和体外实验（29个荷包花科样本和6个外类群样本）中对其进行了验证。在这两种情况下，数据都使我们能够获得可靠的系统发育估计。
我们的结果表明，该诱饵组适用于对荷包花科及其近缘类群的近期和历史样本进行测序，并为进一步研究这个极度多样化属的进化历史打开了新的大门。
